Intelligent optimization management of energy efficiency, as an important part of the intelligent ship, plays an important role in improving the green and intelligent level of ships. To achieve the intelligent optimization management of ship energy efficiency, an intelligent ship is taken as the research object, and an energy efficiency digital twin system that is applicable to intelligent ships is designed. Firstly, the architecture of the energy efficiency digital twin system for the intelligent ship is constructed, including the compositions of the system and the functions of each part based on the requests of the energy efficiency digital twin system. Then, a data-driven ship energy efficiency model is established by utilizing the real-time ship energy efficiency data, which can realize the effective characterization of ship energy efficiency under different navigational conditions. Finally, the energy efficiency digital twin system of the intelligent ship is developed, which can realize the real-time information display, energy efficiency monitoring, dynamic visualization of navigational scenes, and the ship energy efficiency simulation, which is critical to promoting the development of intelligent ships.